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Where are we now? Views of the genome data wars from the field.

0000-0001-6444-1436

@SCEdmunds

scott@gigasciencejournal.com

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Circa 2002: Genome Wars pt. II

Rice was a key battle between the Bermuda & Fort Lauderdale meetings.

Commercial (syngenta) v academic research community.

Like Celera paper, Science again willing to publish genome without data in public domain.

https://www.newscientist.com/article/dn2061-fears-over-rice-genome-access/

Genome Wars: the Empire Strikes Back"A maximum of 15 Kb of DNA or 15 K amino acids can be submitted in a FASTA format, and appropriate BLAST searches will be performed by SBI. Alignment results of the search will be sent via e-mail to the requestor. Rice contigs identified by these alignments can be requested for further analysis using the sequence submission/contig request form. Up to 100 Kb of sequence information may be downloaded per week under your account.”

”TMRI will make its sequence assembly of the whole rice genome available on a CD-ROM under the terms of the Free Public Access Agreement for TMRI Whole Genome Sequence.”

https://web.archive.org/web/20021009130336/http://portal.tmri.org/rice/RiceAccess.html

4Meanwhile in China…

“SciencecongratulatesChinesescientists”

Back to back publication, April 2002

Yu et al., (BGI) & Goff et al. (Syngenta/Myriad), Science 296, 79

BGI data public [AAAA00000000]

Circa 2002: Genome Wars

5 April, 2002 Beijing

http://www.agbioforum.org/v8n23/v8n23a07-pray.htm

Syngenta closed TMRI database, data became part of IRGSP consortium paper published in 2005.

Fort Lauderdale, January 2003.

NAS "UPSIDE: the Uniform Principle for Sharing Integral Data and materials Expeditiously”.

AAAS: “‘All data necessary to understand, assess, and extend the conclusions of the manuscript must be available to any reader of Science’ ”.

Circa 2003: The aftermath

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Rice v Wheat: consequences of publically available genome data.

Papers

http://www.tandfonline.com/doi/abs/10.1080/08109028.2011.631275

Circa 2003-date: The Legacy

IRRI GALAXYRice 3K project: 3,000 rice genomes, 13.4TB public data

Circa 2014: Big Data

8http://www.gigasciencejournal.com/content/3/1/7

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IRRI GALAXYRice 3K project: 3,000 rice genomes, 120 TB public data

Circa 2015: Bigger Data

https://aws.amazon.com/public-data-sets/3000-rice-genome/

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http://www.gigasciencejournal.com/content/3/1/23http://www.gigasciencejournal.com/content/4/1/19

Compute publishing: Virtual Machines

• Downloadable as virtual harddisk/available as Amazon Machine

Image

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http://www.gigasciencejournal.com/content/4/1/33http://www.gigasciencejournal.com/content/4/1/47

Compute publishing: Containers

• Archived docker images/available v dockerhub & bioboxes registry

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Compute publishing: consequences?

• Cost us $1000 AWS credits to

review one paper. Scalable?

• Is the era of free open-data

over?

• Are we happy with AWSification

of research? Research-as-a-

Service?

• If not, who will pay?